Summary of this application - MSI-T¶

The Leginon "MSI T" application is essentially a duplicate of "MSI" except that the Hole Finder nodes have been replaced by JAHC Finder (Template Hole Finder) nodes. The new hole finder eliminates the edge finding which has been shown to perform poorly when the ice is thick and replace the ring template used in correlation with a template image of the the hole. Therefore, the users should follow the MSI setup and operation and consult this chapter when it comes to Hole Targeting and Exposure Targeting. We have the plan to consolidate the hole finders into one, but not in this version, yet.

<link linkend="preleg1setup">Pre-MSI Set-up</link>: Prior to setting up Leginon for the day, make sure that Leginon has been previously set-up (this step is in case the ambitious user decides to proceed to this section for the first time and hasn't gone through all the calibrations...).

<link linkend="MSI_pref">MSI preference & configuration</link>: The comprehensive MSI preferences and configuration example. The node name change in MSI raster are: "Hole Targeting" -> "Sub-Square Targeting" and "Hole" -> "Sub-Square".

<link linkend="MISQuickStart">MSI Quick Start checklist</link>: A short check list for users who are familiar with the application and have saved preferences.

<link linkend="MSISetupDetails">MSI set-up in more details</link>: The more complicated MSI Leginon application set-up that should be completed before collecting data.

<link linkend="MSISetupDetails">Queuing option</link>: An option that groups human interaction together by putting the submitted targets from different images at the same level of target finders into a queue and process them later.

<link linkend="MSI_troubleshooting">Trouble shooting</link>: This trouble shooting sections addresses some of the possible challenges a Leginon user may face.

In this chapter:

<link linkend="MSITsetup">Raster Finder nodes set-up</link>: A short guide to set-up the raster finder nodes in the MSI raster Leginon application.

NOTE: JAHC stands for Joel's Amazing Holey Carbon, the experimental holed carbon support that is now sold as C-flat from Protochips Inc. Since it lacks the lips around the hole, this hole finder is especially useful.